SGD Help: Physical and Genetic Maps
Physical and Genetic Maps, SGD has two different sets of genetic maps: The Combined Physical and Genetic Maps contain genetically and/or physcially mapped ORFs and display a side by side representation of the physical and genetic maps for individual chromosomes; The Genetic Distance vs. Physical Distance Ratio Maps displays a calculation of relative recombination frequencies, based on 2-point data available from SGD and the lengths of DNA sequences in the genome.
- Combined Physical and Genetic Maps
- Genetic Distance vs. Physical Distance Ratios
The Combined Physical and Genetic Map for an individual chromosome is a side by side representation of the physical and genetic maps for the chromosome. It contains genetically and/or physically mapped genes.
The Combined Physical and Genetic Maps are derived from the systematic genomic sequencing data and from data contained within SGD (Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 387(6632S):67-73 (1997)), as well as data presented in earlier reviews (Mortimer and Schild Microbiol. Rev. 44:519-571 (1980), Microbiol. Rev. 49:181-213 (1985), Mortimer et al., Yeast 5:321-404 (1989), Mortimer et al., Yeast 8:817-902 (1992)). In the case where an ORF has been defined, its standard gene name is indicated.
- Physical and Genetic Map positions - The Physical Map is on the left (in Kbp) and the Genetic Map is on the right (in cM). Correspondingly, the Kbp scale is on the left side of the window and the cM scale is on its right side.
- ORF Identification on the Physical Map - ORFs are identified by blue (Crick strand) and red (Watson strand) bars on the physical map. The ORF boxes on the left of the physical map line are for ORFs which have been mapped physically, but not genetically (i.e. gene B in the display). The boxes to the right of the physical map line are for those ORFs which have been mapped both physically and genetically (i.e. genes A and C in the display).
- ORF Labelling - All identified ORFs are present as bars on the Combined Genetic and Physical Map. In the case where an ORF has been defined, its primary gene name is present on the map. ORFs without gene names are represented only by bars on the map. In order to identify the ORF name for a bar which is not labelled on the map, run the cursor over the bar and look at the linking URL address at the bottom of the page.
- ORF Identification on the Genetic Map - ORFs are identified on the genetic map by horizontal tick marks to the right of the genetic map.
- Lines connecting the Physical and Genetic Maps - Lines connect genetically mapped genes with their ORFs on the physical map. In this case, the line extends from the top of the ORF's colored box on the physical map to the corresponding tick mark on the genetic map (see genes A and C for an example).
- Getting to the Locus Summary page - The Locus Summary page can be found for any of the ORFs or centromeres displayed by clicking on the desired ORF name, red or blue bars, or the centromeres.
- Overlapping ORFs - In the case of overlapping ORFs, the element at the bottom is shown to overlap the element at the top.
The Combined Physical and Genetic Maps can be accessed by:
- Clicking one of the sixteen chromosome numbers at the top of the Sample Map to display the Combined Physical and Genetic Map for a desired chromosome
- Clicking the "Physical and Genetic Map" link at the bottom of the Chromosomal Features Map display
This display graphs the length of a chromosome along the x-axis (in kilobasepairs) and the ratio of centimorgans to kilobasepairs along the y-axis (example below). Since the location in centimorgans is not known for every locus, intervals are graphed. For example, if marker A is 15 kilobasepairs away from its closest genetically mapped locus, marker B, there will be a 15 kilobasepair-long plateau with the cM/Kbp value that is calculated for that genetic interval.
Representative genetically mapped loci and their postions in cM are indicated at the top of the figure. The "Zoom In" bar lets you magnify the display region. After zooming in, blue arrows that point to the left or to the right of the figure allow you to scroll to the left or right along the chromosome. Note that there is no "zoom out" feature; to zoom out use the "back" button of your browser. The Genetic versus Physical Distance Ratio for chromosome I is shown below.
At the bottom of the Combined Physical and Genetic Maps of S. cerevisiae page, there is a table that lets you display the Genetic Distance vs. Physical Distance Ratios for any chromosome (see below). Just click on the red chromosome above the overall centimorgans/kilobasepairs (cM/Kbp) calculation for the chromosome.